Histone H1 inSaccharomyces cerevisiae

Ushinsky, Sophia; Bussey, Howard; Ahmed, Aisha; Wang, Y.; Friesen, James D.; Williams, B. A.; Storms, Reginald

doi:10.1002/(sici)1097-0061(199702)13:2<151::aid-yea94>3.0.co;2-5

Cited by 92 publications

(9 citation statements)

References 24 publications

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“…In Drosophila , Neurospora crassa , and mammalian cells, H1 deposition is part of a crosstalk with the epigenetic landscape, notably DNA methylation [10–12] and histone H3 methylation [12–14]. Given the profound impact of H1 proteins on chromatin organization, it is surprising that H1 depletion is tolerated in some organisms: this is the case of Tetrahymena , yeast, fungi, worms [15–19]. However, in mouse and Drosophila , it impairs viability [10, 20].…”

Section: Introductionmentioning

confidence: 99%

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

et al. 2019

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Background Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis , while H1 is known to influence heterochromatin and DNA methylation, its contribution to transcription, molecular, and cytological chromatin organization remains elusive. Results We provide a multi-scale functional study of Arabidopsis linker histones. We show that H1-deficient plants are viable yet show phenotypes in seed dormancy, flowering time, lateral root, and stomata formation—complemented by either or both of the major variants. H1 depletion also impairs pluripotent callus formation. Fine-scale chromatin analyses combined with transcriptome and nucleosome profiling reveal distinct roles of H1 on hetero- and euchromatin: H1 is necessary to form heterochromatic domains yet dispensable for silencing of most transposable elements; H1 depletion affects nucleosome density distribution and mobility in euchromatin, spatial arrangement of nanodomains, histone acetylation, and methylation. These drastic changes affect moderately the transcription but reveal a subset of H1-sensitive genes. Conclusions H1 variants have a profound impact on the molecular and spatial (nuclear) chromatin organization in Arabidopsis with distinct roles in euchromatin and heterochromatin and a dual causality on gene expression. Phenotypical analyses further suggest the novel possibility that H1-mediated chromatin organization may contribute to the epigenetic control of developmental and cellular transitions. Electronic supplementary material The online version of this article (10.1186/s13059-019-1767-3) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

et al. 2019

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“…On sequencing the entire yeast genome a sequence of an open reading frame (ORF) with similarity to the globular domain of linker histones has been identified, and the gene has been interpreted as the H1 histone gene (Hho1) of yeast [16]. Deletion of the gene in Saccharomyces cerevisiae had no significant phenotypic effect [17, 18], except that the expression of β‐galactosidase from a cytochrome c ‐lacZ reporter plasmid was altered [19]. Although recombinantly expressed Hho1p binds in vitro to the linker DNA of reconstituted core dinucleosomes [18], until now no specific linker histone in vivo function has been ascribed to this protein, and it cannot be excluded that the H1‐like protein is rather a gene specific transcription factor, like the linker histone structural homologue HNF3‐γ [20], than a standard linker histone.…”

Section: Introductionmentioning

confidence: 99%

Heterologous expression of human H1 histones in yeast

et al. 1998

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The complete set of seven human H1 histone subtype genes was heterologously expressed in yeast. Since Saccharomyces cerevisiae lacks standard histone H1 we could isolate each recombinantly expressed human H1 subtype in pure form without contamination by endogenous H1 histones. For isolation of the H1 histones in this expression system no tagging was needed and the isoforms could be extracted with the authentic primary structure by a single extraction step with 5% (0.74 M) perchloric acid. The isolated H1 histone proteins were used to assign the subtype genes to the corresponding protein spots or peaks after two-dimensional gel electrophoresis and capillary zone electrophoresis, respectively. This allowed us to correlate transcriptional data with protein data, which was barely possible until now.z 1998 Federation of European Biochemical Societies.

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“…Localization not only was consistent with the expected organelle compartments but also reflects responses to different nutrient types. We found several interesting patterns after transfer to nitrogen-deficient (Y-D) medium that may be associated with stationary phase such as histone H1, important for DNA packaging [93]. Erg6 is a protein in the ergosterol biosynthetic pathway, used as a lipid droplet marker, and a target of antifungals [94, 95].…”

Section: Resultsmentioning

confidence: 99%

A molecular genetic toolbox for Yarrowia lipolytica

Bredeweg

Pomraning

Dai

et al. 2017

Biotechnol Biofuels

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Background Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain.ResultsWe have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the “Yarrowia lipolytica Cell Atlas,” a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells.ConclusionsThese molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0687-7) contains supplementary material, which is available to authorized users.

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Histone H1 inSaccharomyces cerevisiae

Cited by 92 publications

References 24 publications

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

Heterologous expression of human H1 histones in yeast

A molecular genetic toolbox for Yarrowia lipolytica

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